Identification and Expression Analysis of the B-box Transcription Factor Family in Pepper

doi:10.16420/j.issn.0513-353x.2020-0600

Acta Horticulturae Sinica ›› 2021, Vol. 48 ›› Issue (5): 987-1001.doi: 10.16420/j.issn.0513-353x.2020-0600

• Research Papers • Previous Articles Next Articles

Identification and Expression Analysis of the B-box Transcription Factor Family in Pepper

HU Jingtao^*(), RUAN Yu, GAN Liping

College of Biology and Food Engineering,Chongqing Three Gorges University,Wanzhou,Chongqing 404100,China

Received:2021-02-23 Revised:2021-03-19 Online:2021-05-25 Published:2021-06-07

Abstract

Abstract:

Based on the genome data of pepper,the chromosomal localization,gene structure,phylogenetic relationships and tissue-specific expression of B-box genes in pepper were analyzed by bioinformatics method. Moreover,the transcription level of the family genes under hormone and abiotic stress was detected by qRT-PCR. A total of 26 BBX members,which were distributed on 12 chromosomes,have been identified in pepper genome. Phylogenetic analysis showed that the CaBBX proteins could further be divided into five groups:groupⅠ-Ⅴ. Among them,members in groupⅠcontains two B-box domains. All the proteins in groupⅡandⅢcontained B-box1,B-box2 and CCT domains,except for CaBBX25. The proteins in group Ⅳ only had a B-box domain while members in group Ⅴ contained a B-box and a CCT domain. A same or similar number of exons has been found in members of the same clade usually. At the same time,a higher similar of the composition of motifs was also observed. Tissue specific expression analysis showed that the other 17 genes were highly expressed in different organs or at different devolpment stages of fruits,except for the class D genes. The result of qRT-PCR showed that 10 CaBBX genes could be promoted or repressed by the hormones and abiotic stresses.

Key words: pepper, B-box transcription factor, identification, expression analysis

CLC Number:

S641.3

HU Jingtao, RUAN Yu, GAN Liping. Identification and Expression Analysis of the B-box Transcription Factor Family in Pepper[J]. Acta Horticulturae Sinica, 2021, 48(5): 987-1001.

Figures/Tables 9

References 38

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基因 Gene	引物序列(5′-3′) Primer sequence		产物大小/bp Product length
CaBBX1	F:TTGGGGATTTTGCTCCTACTAAG;	R:GCCTTAGATGTTCCATTGTCCA	142
CaBBX2	F:AAAGTCGCCTCCCATTCAGA;	R:GCAAAATCCCCAGTCTCGC	132
CaBBX3	F:TGGCAAGTAAGCATCAGAGGC;	R:TAGGAATCGCTGGTGGTTCTTAG	182
CaBBX4	F:CTCCACCTCCTCAGAAGAATCAG;	R:GAAGGAAATGGAAGATGGGCTA	170
CaBBX5	F:ATCTGTCAGGAAAGGAGGGCT;	R:AAGGTATCTGTTGTGCTTCTGAGTG	120
CaBBX6	F:TTTTCTGCTGGATGTAAACCTTTT;	R:TACCTCAATACTCTTGCTTCCCTG	206
CaBBX7	F:CTTGTGAGCAGGGGATGGG;	R:CAAAGGGGCAGACTTGACTAAAT	149
CaBBX8	F:AGACAGAGAAGCAAGAGTTTTACGA;	R:GTGCCCGATAAAATCTCCGT	211
CaBBX9	F:AATCTCACAATGCTCCCACTACTG;	R:CGAGCCTTCCTTGACTCATACC	163
CaBBX10	F:TCCATTACTGCCTCTGCTCGT;	R:ACATTTCCCTGCCAATCACTACT	185
CaUBI3	F:CTGGAGGTGTATTTTTGGTTTCA;	R:CAACAGAGAGCAGATGGACAGC	215

基因 Gene	引物序列(5′-3′) Primer sequence		产物大小/bp Product length
CaBBX1	F:TTGGGGATTTTGCTCCTACTAAG;	R:GCCTTAGATGTTCCATTGTCCA	142
CaBBX2	F:AAAGTCGCCTCCCATTCAGA;	R:GCAAAATCCCCAGTCTCGC	132
CaBBX3	F:TGGCAAGTAAGCATCAGAGGC;	R:TAGGAATCGCTGGTGGTTCTTAG	182
CaBBX4	F:CTCCACCTCCTCAGAAGAATCAG;	R:GAAGGAAATGGAAGATGGGCTA	170
CaBBX5	F:ATCTGTCAGGAAAGGAGGGCT;	R:AAGGTATCTGTTGTGCTTCTGAGTG	120
CaBBX6	F:TTTTCTGCTGGATGTAAACCTTTT;	R:TACCTCAATACTCTTGCTTCCCTG	206
CaBBX7	F:CTTGTGAGCAGGGGATGGG;	R:CAAAGGGGCAGACTTGACTAAAT	149
CaBBX8	F:AGACAGAGAAGCAAGAGTTTTACGA;	R:GTGCCCGATAAAATCTCCGT	211
CaBBX9	F:AATCTCACAATGCTCCCACTACTG;	R:CGAGCCTTCCTTGACTCATACC	163
CaBBX10	F:TCCATTACTGCCTCTGCTCGT;	R:ACATTTCCCTGCCAATCACTACT	185
CaUBI3	F:CTGGAGGTGTATTTTTGGTTTCA;	R:CAACAGAGAGCAGATGGACAGC	215

名称 Name	蛋白/aa Proten length	分子量 Molecular weight	等电点 PI	不稳定指数 Instability index	脂肪系数 Aliphatic index	亲水性值 Hydropathicity
CaBBX1	297	32 012.77	4.98	54.36	66.70	-0.377
CaBBX2	299	32 173.20	4.97	52.19	71.51	-0.269
CaBBX3	233	25 979.56	5.00	52.79	78.37	-0.415
CaBBX4	305	33 860.88	6.24	54.56	68.39	-0.443
CaBBX5	319	35 220.55	6.50	55.21	70.25	-0.497
CaBBX6	343	37 932.28	5.45	51.27	65.98	-0.493
CaBBX7	414	45 344.37	5.48	56.84	58.41	-0.535
CaBBX8	384	42 540.99	6.56	40.78	72.86	-0.345
CaBBX9	387	43 342.99	5.45	55.93	57.18	-0.755
CaBBX10	469	51 670.91	6.75	48.26	66.59	-0.637
CaBBX11	267	29 831.52	5.62	46.30	78.91	-0.431
CaBBX12	212	23 515.68	6.17	56.08	71.79	-0.559
CaBBX13	356	39 425.86	5.29	45.15	64.66	-0.499
CaBBX14	404	44 556.35	5.41	39.93	63.76	-0.634
CaBBX15	407	45 394.43	5.32	44.63	67.59	-0.636
CaBBX16	398	43 889.44	5.27	41.34	62.04	-0.637
CaBBX17	426	46 866.13	5.07	52.81	60.68	-0.593
CaBBX18	409	45 276.46	5.27	61.89	57.48	-0.595
CaBBX19	411	46 715.66	5.26	50.78	61.29	-0.856
CaBBX20	171	18 935.07	4.39	51.21	48.42	-0.932
CaBBX21	470	53 535.89	5.21	41.38	69.49	-0.713
CaBBX22	247	27 399.14	4.60	53.57	57.29	-0.745
CaBBX23	201	22 041.04	4.49	57.37	58.21	-0.705
CaBBX24	247	27 712.80	9.17	63.21	76.64	-0.279
CaBBX25	491	54 983.39	6.00	57.73	68.15	-0.665
CaBBX26	182	20 146.89	6.78	44.30	66.98	-0.554
名称 Name	基因登录号 Gene locus ID			亚细胞定位 Subcellular localization
CaBBX1	XM_016725607.1/Capana07g002062			nucl:13,cyto:1
CaBBX2	XM_016685612.1/Capana09g000394			nucl:11,chlo:1,cyto:1,extr:1
CaBBX3	XM_016722599.1/Capana06g000735			nucl:7,cyto:2,plas:2,cysk:2,chlo:1
CaBBX4	XM_016715935.1/Capana04g000266			nucl:8,cyto:3,chlo:2,extr:1
CaBBX5	XM_016696615.1/Capana12g000659			nucl:11,chlo:1,cyto:1,extr:1
CaBBX6	XM_016693601.1/Capana01g004030			chlo:13,nucl:1
CaBBX7	XM_016724939.1/Capana07g001114			nucl:14
CaBBX8	XM_016724136.1/Capana07g000030			cyto:5,nucl:3,chlo:2,extr:2,cysk:2
CaBBX9	XM_016710217.1/Capana03g003558			nucl:11,chlo:1,plas:1,vacu:1
CaBBX10	XM_016699689.1/Capana00g001486			nucl:14
CaBBX11	XM_016684335.1/Capana08g002611			nucl:7,cyto:3,chlo:2,extr:1,vacu:1
CaBBX12	XM_016684347.1/Capana08g002625			cyto:5,chlo:3,nucl:3,cysk_plas:2,plas:1.5,cysk:1.5
CaBBX13	XM_016696444.1/Capana12g000414			chlo:11,nucl:2,cyto:1
CaBBX14	XM_016705720.1/Capana02g003199			nucl:9,chlo:5
CaBBX15	XM_016705721.1/Capana02g003201			chlo:7,nucl:6,cyto:1
CaBBX16	XM_016705722.1/Capana02g003200			nucl:13,plas:1
CaBBX17	XM_016697126.1/Capana00g004489			nucl:13,mito:1
CaBBX18	XM_016699024.1/Capana00g004028			nucl:14
CaBBX19	XM_016707287.1/Capana03g000377			nucl:10,chlo:2,mito:1,cysk:1
CaBBX20	XM_016706590.1/CA02g17080			nucl:8,chlo:3,cyto:1,mito:1,plas:1
CaBBX21	XM_016693241.1/Capana11g002294			chlo:4,nucl:4,cyto:2,mito:2,plas:1,cysk:1
CaBBX22	XM_016725230.1/Capana07g001588			chlo:9,mito:3,nucl:2
CaBBX23	XM_016690415.1/Capana10g000048			nucl:13,mito:1
CaBBX24	XM_016700813.1/Capana00g004911			nucl:8,cyto:4,extr:2
CaBBX25	XM_016717318.1/Capana05g001195			nucl:13,mito:1
CaBBX26	XM_016705057.1/Capana02g002620			cyto:12,plas:1,cysk:1

名称 Name	蛋白/aa Proten length	分子量 Molecular weight	等电点 PI	不稳定指数 Instability index	脂肪系数 Aliphatic index	亲水性值 Hydropathicity
CaBBX1	297	32 012.77	4.98	54.36	66.70	-0.377
CaBBX2	299	32 173.20	4.97	52.19	71.51	-0.269
CaBBX3	233	25 979.56	5.00	52.79	78.37	-0.415
CaBBX4	305	33 860.88	6.24	54.56	68.39	-0.443
CaBBX5	319	35 220.55	6.50	55.21	70.25	-0.497
CaBBX6	343	37 932.28	5.45	51.27	65.98	-0.493
CaBBX7	414	45 344.37	5.48	56.84	58.41	-0.535
CaBBX8	384	42 540.99	6.56	40.78	72.86	-0.345
CaBBX9	387	43 342.99	5.45	55.93	57.18	-0.755
CaBBX10	469	51 670.91	6.75	48.26	66.59	-0.637
CaBBX11	267	29 831.52	5.62	46.30	78.91	-0.431
CaBBX12	212	23 515.68	6.17	56.08	71.79	-0.559
CaBBX13	356	39 425.86	5.29	45.15	64.66	-0.499
CaBBX14	404	44 556.35	5.41	39.93	63.76	-0.634
CaBBX15	407	45 394.43	5.32	44.63	67.59	-0.636
CaBBX16	398	43 889.44	5.27	41.34	62.04	-0.637
CaBBX17	426	46 866.13	5.07	52.81	60.68	-0.593
CaBBX18	409	45 276.46	5.27	61.89	57.48	-0.595
CaBBX19	411	46 715.66	5.26	50.78	61.29	-0.856
CaBBX20	171	18 935.07	4.39	51.21	48.42	-0.932
CaBBX21	470	53 535.89	5.21	41.38	69.49	-0.713
CaBBX22	247	27 399.14	4.60	53.57	57.29	-0.745
CaBBX23	201	22 041.04	4.49	57.37	58.21	-0.705
CaBBX24	247	27 712.80	9.17	63.21	76.64	-0.279
CaBBX25	491	54 983.39	6.00	57.73	68.15	-0.665
CaBBX26	182	20 146.89	6.78	44.30	66.98	-0.554
名称 Name	基因登录号 Gene locus ID			亚细胞定位 Subcellular localization
CaBBX1	XM_016725607.1/Capana07g002062			nucl:13,cyto:1
CaBBX2	XM_016685612.1/Capana09g000394			nucl:11,chlo:1,cyto:1,extr:1
CaBBX3	XM_016722599.1/Capana06g000735			nucl:7,cyto:2,plas:2,cysk:2,chlo:1
CaBBX4	XM_016715935.1/Capana04g000266			nucl:8,cyto:3,chlo:2,extr:1
CaBBX5	XM_016696615.1/Capana12g000659			nucl:11,chlo:1,cyto:1,extr:1
CaBBX6	XM_016693601.1/Capana01g004030			chlo:13,nucl:1
CaBBX7	XM_016724939.1/Capana07g001114			nucl:14
CaBBX8	XM_016724136.1/Capana07g000030			cyto:5,nucl:3,chlo:2,extr:2,cysk:2
CaBBX9	XM_016710217.1/Capana03g003558			nucl:11,chlo:1,plas:1,vacu:1
CaBBX10	XM_016699689.1/Capana00g001486			nucl:14
CaBBX11	XM_016684335.1/Capana08g002611			nucl:7,cyto:3,chlo:2,extr:1,vacu:1
CaBBX12	XM_016684347.1/Capana08g002625			cyto:5,chlo:3,nucl:3,cysk_plas:2,plas:1.5,cysk:1.5
CaBBX13	XM_016696444.1/Capana12g000414			chlo:11,nucl:2,cyto:1
CaBBX14	XM_016705720.1/Capana02g003199			nucl:9,chlo:5
CaBBX15	XM_016705721.1/Capana02g003201			chlo:7,nucl:6,cyto:1
CaBBX16	XM_016705722.1/Capana02g003200			nucl:13,plas:1
CaBBX17	XM_016697126.1/Capana00g004489			nucl:13,mito:1
CaBBX18	XM_016699024.1/Capana00g004028			nucl:14
CaBBX19	XM_016707287.1/Capana03g000377			nucl:10,chlo:2,mito:1,cysk:1
CaBBX20	XM_016706590.1/CA02g17080			nucl:8,chlo:3,cyto:1,mito:1,plas:1
CaBBX21	XM_016693241.1/Capana11g002294			chlo:4,nucl:4,cyto:2,mito:2,plas:1,cysk:1
CaBBX22	XM_016725230.1/Capana07g001588			chlo:9,mito:3,nucl:2
CaBBX23	XM_016690415.1/Capana10g000048			nucl:13,mito:1
CaBBX24	XM_016700813.1/Capana00g004911			nucl:8,cyto:4,extr:2
CaBBX25	XM_016717318.1/Capana05g001195			nucl:13,mito:1
CaBBX26	XM_016705057.1/Capana02g002620			cyto:12,plas:1,cysk:1

Identification and Expression Analysis of the B-box Transcription Factor Family in Pepper

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